In this article, a new data‐based iterative learning control (ILC) algorithm is proposed via Gaussian process regression (GPR) to accomplish the trajectory tracking objective of aircraft subject to completely unknown dynamics and strong nonlinearities. The nonlinear system input–output relationship of the unknown aircraft is formulated through GPR by leveraging historical data, based on which an optimal ILC framework is established. The monotonic convergence analysis of the GPR‐based ILC is explored such that high‐precision tracking tasks can be accomplished without prior model knowledge. Simulation tests are further conducted on a commercial aircraft performing a continuous climb operation to illustrate the effectiveness of the GPR‐based ILC approach.